Under the construction of ecological civilization in China, the contradiction between resource depletion and sustainable development is becoming a crucial issue nowadays. Based on resources and socioeconomic statistics, this paper applied the modified three-dimensional ecological footprint (3DEF) model to analyze and evaluate natural capital utilization in China during 2009-2016. The results showed that ecological footprint size (EF_size) differed within 34 provinces and ecological footprint depth (EF_depth) far exceeded the original value of 1.00. EF_size per capita decreased first and then increased with obvious spatial heterogeneity in 34 provinces. The highest EF_size was in Tibet (10.87-12.35 hm²/cap) and the lowest in Macao (0.02 hm²/cap), while natural capital flow ratios were greatly insufficient in Guangxi (47.68%-67.34%) and Shanghai (66.31%-68.88%). The highest EF_depth occurred in Hong Kong (19.24-26.02), followed by Macao (8.60-10.88) and Ningxia (4.60-7.46), which were extremely above the average of China while Tibet registered the lowest value (1.64-1.79). Cropland and fossil energy land contributed the most to total ecological deficit while woodland component maintained in ecological surplus state during the study period. Spatial patterns of natural capital utilization in 34 provinces were divided into four categories through clustering analysis integrated with ArcGIS software. The significance of this research is optimizing 3DEF model applied to 34 provinces in China systematically. The investigation also quantitatively depicted natural capital flow and stock utilization on provincial scale and further explored their influencing socioeconomic factors. Overall, our findings could provide basic data and guidance for decision-makers to establish regional sustainability strategies in China.